Unit

UNIT 7.5 Using GenMAPP and MAPPFinder to View Microarray Data on Biological Pathways and Identify Global Trends in the Data

  1. Kam D. Dahlquist

Published Online: 1 MAY 2004

DOI: 10.1002/0471250953.bi0705s05

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Dahlquist, K. D. 2004. Using GenMAPP and MAPPFinder to View Microarray Data on Biological Pathways and Identify Global Trends in the Data. Current Protocols in Bioinformatics. 5:7.5:7.5.1–7.5.26.

Author Information

  1. Vassar College, Poughkeepsie, New York

Publication History

  1. Published Online: 1 MAY 2004
  2. Published Print: MAR 2004

Abstract

GenMAPP (Gene MicroArray Pathway Profiler) is a free, stand-alone computer program designed for viewing and analyzing gene expression data on MAPPs representing biological pathways or any other functional grouping of genes. A MAPP is a special file format produced with the graphics tools in GenMAPP that depicts the biological relationship between genes or gene products. When a MAPP is linked to an expression dataset, GenMAPP automatically and dynamically color-codes the genes on the MAPP according to criteria supplied by the user. MAPPFinder is an accessory program that works with GenMAPP and the annotations from the Gene Ontology (GO) Consortium to identify global biological trends in gene expression data. MAPPFinder relates the microarray dataset to the GO hierarchy and calculates a percentage and statistical score for genes meeting the user's criterion for a meaningful gene expression change for each GO biological process, cellular component, and molecular function term.

Keywords:

  • GenMAPP;
  • MAPPFinder;
  • microarray;
  • pathways;
  • Gene Ontology;
  • gene expression profile